Allozyme variation was studied by Peterson and Heaney (1993) and Heaney et al. (2005). Substantial geographic mtDNA variation is evident in this species (Trina Roberts 2005 PhD thesis). In this account we include Sibuyan population within this species, although it was listed separately by Heaney et al. (1998).

Justification:H. fischeri is assessed as Least Concern as it is common and widespread at higher elevations where threats to the species are minimal. It is tolerant of degraded habitats and occurs in a number of protected areas; its population is unlikely to be significantly declining.

This is one of the most common fruit bats in primary forest, especially at middle elevations; H. fischeri is often moderately common in secondary forest, and is also present in mixed agricultural habitats and second-growth forest (Heaney et al. 1998). Within forest the species abundance usually increases with elevation up to about 1,200-1,500 m asl, and then declines (Heaney et al. 1989, 1991, 1998, 2006; Heideman and Heaney 1989, Rickart et al. 1993). Patterns of abundance on Luzon are similar to those on other islands, but they are less abundant there overall. In a 2003 mist net survey on Mount Apo, Mindanao, Haplonycteris fischeri was common at lower elevation mossy-montane forest that had been subjected to habitat alteration (Godfrey et al. unpublished report).

The Philippine pygmy fruit bat inhabits lowland and montane, primary and secondary habitats, including mossy forest, and mixed agricultural habitats and second-growth forest. It exhibits an eight month delay in embryo development which gives a gestation period of 11.5 months, the longest known in bats (Heideman 1989). Females can become pregnant at the age of three to five months (Heideman 1989). The species is an important seed distributer.

There are no major threats to H. fischeri, although populations, particularly those in the lowlands, have declined in recent decades as a result of habitat destruction by logging, and conversion to intensive agriculture, whereas highland populations have not been so badly affected (L. Heaney pers. comm. 2006).